From e58b6e677d3d0420ccd91783a5683c4e7ab91a45 Mon Sep 17 00:00:00 2001 From: Dan Birman Date: Fri, 11 Sep 2026 10:18:46 -0700 Subject: [PATCH 1/3] refactor: improve table of contents to make find data page easier to find --- docs/source/acquire_upload/index.md | 4 ---- docs/source/explore_analyze/index.md | 4 ---- docs/source/index.md | 21 +++------------------ 3 files changed, 3 insertions(+), 26 deletions(-) diff --git a/docs/source/acquire_upload/index.md b/docs/source/acquire_upload/index.md index f98706e..8d465df 100644 --- a/docs/source/acquire_upload/index.md +++ b/docs/source/acquire_upload/index.md @@ -1,7 +1,3 @@ ---- -orphan: true ---- - # Acquire, upload & process ## I want to... diff --git a/docs/source/explore_analyze/index.md b/docs/source/explore_analyze/index.md index fdd60f0..6493641 100644 --- a/docs/source/explore_analyze/index.md +++ b/docs/source/explore_analyze/index.md @@ -1,7 +1,3 @@ ---- -orphan: true ---- - # Explore, QC & analyze Raw assets uploaded from platforms at AIND are run through automated pipelines that produce derived assets. You can explore these assets through the [Data Portal](https://data.allenneuraldynamics.org/assets). diff --git a/docs/source/index.md b/docs/source/index.md index afe57cb..ee6e729 100644 --- a/docs/source/index.md +++ b/docs/source/index.md @@ -48,25 +48,10 @@ Follow these links to request access to: ```{toctree} :maxdepth: 1 :hidden: -:caption: Acquire, upload & process +:caption: How-to -acquire_upload/prepare_before_acquisition -acquire_upload/acquire_data -acquire_upload/calibration -acquire_upload/upload_data -acquire_upload/process_data - -``` - -```{toctree} -:maxdepth: 1 -:hidden: -:caption: Explore, QC & analyze - -explore_analyze/quality_control -explore_analyze/find_data -explore_analyze/analyze_data -explore_analyze/outreach +acquire_upload/index +explore_analyze/index ``` From a56e660db9351ed7a21c02b94d0b21b7dc819359 Mon Sep 17 00:00:00 2001 From: Dan Birman Date: Fri, 11 Sep 2026 10:22:20 -0700 Subject: [PATCH 2/3] docs: remove redundant/outdated dashboard links --- docs/source/explore_analyze/find_data.md | 7 ------- 1 file changed, 7 deletions(-) diff --git a/docs/source/explore_analyze/find_data.md b/docs/source/explore_analyze/find_data.md index 323bb8d..8b817d1 100644 --- a/docs/source/explore_analyze/find_data.md +++ b/docs/source/explore_analyze/find_data.md @@ -97,10 +97,3 @@ records = client.retrieve_docdb_records( ``` More details about DocDB queries can be found in the [aind-data-access-api#querying-metadata documentation](https://aind-data-access-api.readthedocs.io/en/latest/ExamplesDocDBRestApi.html#querying-metadata) - -## Dashboards - -We are expanding the number of platform and project dashboards based on V2 metadata over time. We currently host: - -- [data portal](https://data.allenneuraldynamics.org/assets) is a tool for finding and exploring data assets. Currently, you can search all assets that have V2 metadata and easily click links to go to the Code Ocean data asset, metadata, and QC report. -- [smartspim dashboard](https://data.allenneuraldynamics-test.org/smartspim) From 30b0298486b8b0daee67c00af765c50f8952e642 Mon Sep 17 00:00:00 2001 From: Dan Birman Date: Fri, 11 Sep 2026 10:24:47 -0700 Subject: [PATCH 3/3] docs: add missing platforms --- docs/source/explore_analyze/index.md | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/docs/source/explore_analyze/index.md b/docs/source/explore_analyze/index.md index 6493641..724bd35 100644 --- a/docs/source/explore_analyze/index.md +++ b/docs/source/explore_analyze/index.md @@ -12,9 +12,12 @@ There are also Platform dashboards for each of the major platforms in Neural Dyn | Platform | Dashboard | Internal Site | | -- | -- | -- | -| SmartSPIM | [Dashboard](https://data.allenneuraldynamics.org/smartspim) | [Internal Site](https://alleninstitute.sharepoint.com/sites/NeuralDynamics/SitePages/SmartSPIM-Platform.aspx) | -| Fiber Photometry | [Dashboard](https://data.allenneuraldynamics.org/fiber_photometry) | [Internal site](https://alleninstitute.sharepoint.com/sites/NeuralDynamics/SitePages/Fiber-Photometry-Platform.aspx) | +| ExaSPIM | [Dashboard](https://data.allenneuraldynamics.org/exaspim) | | | Dynamic Foraging | [Dashboard](https://data.allenneuraldynamics.org/dynamic_foraging)| | +| Dynamic Routing | [Dashboard](https://data.allenneuraldynamics.org/dynamic_routing)| | +| Fiber Photometry | [Dashboard](https://data.allenneuraldynamics.org/fiber_photometry) | [Internal site](https://alleninstitute.sharepoint.com/sites/NeuralDynamics/SitePages/Fiber-Photometry-Platform.aspx) | +| SLAP2 | [Dashboard](https://data.allenneuraldynamics.org/slap2) | | +| SmartSPIM | [Dashboard](https://data.allenneuraldynamics.org/smartspim) | [Internal Site](https://alleninstitute.sharepoint.com/sites/NeuralDynamics/SitePages/SmartSPIM-Platform.aspx) | | VR Foraging | [Dashboard](https://data.allenneuraldynamics.org/vr_foraging) | | ## I want to...